NAR2020 data-repository

This project includes simulation data of the Gd-II riboswitch.

Publication Information:

Title: Guanidine-II Aptamer Conformations and Ligand Binding Modes through the Lens of Molecular Simulation

Authors: Jakob Steuer, Oleksandra Kukharenko, Kai Riedmiller, Joerg S. Hartig and Christine Peter

Journal: Nucleic Acids Research, Volume 49, Issue 14, Pages 7954–7965

Date: 20 August 2021

DOI: 10.1093/nar/gkab592

Data Information:

Forcefield: DESRES RNA force field, implemented by Bussi, G. here from Tan et al, PNAS 2018.:

• forcefield.ff

MD Parameter File:

• parameters.mdp

Run Input Files:

• topology_gd.tpr (Simulation with guanidinium)

• topology_nl.tpr (Simulation without ligand)

• topology_ure1.tpr (Simulation with urea, configuration 1)

• topology_ure2.tpr (Simulations with urea, configuration 2)

• topology_ure3.tpr (Simulations with urea, configuration 3)